DAVID Bioinformatics 6.7
The Database for Annotation, Visualization and Integrated Discovery
DAVID Bioinformatics Resources 6.7
National Institute of Allergy and Infectious Diseases (NIAID), NIH
publication
LIB Publications

Last updated in July 2012

2012 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999

2012

1.
X Jiao, BT Sherman, R Stephens, MW Baseler, HC Lane, RA Lempicki. DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics (2012) 28 (13): 1805-1806. doi: 10.1093/bioinformatics/bts251
[PubMed]

2009

1.
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc. 2009;4(1):44-57.
[PubMed]


2.
Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009 Jan;37(1):1-13.
[PubMed]

2008

1.
Barton G, Abbott J, Chiba N, Huang DW, Huang Y, Krznaric M, Mack-Smith J, Saleem A, Sherman BT, Tiwari B, Tomlinson C, Aitman T, Darlington J, Game L, Sternberg MJ, Butcher SA. EMAAS: an extensible grid-based rich internet application for microarray data analysis and management. BMC Bioinformatics. 2008 Nov 25;9:493.
[PubMed]


2.
Read SW, Lempicki RA, Di Mascio M, Srinivasula S, Burke R, Sachau W, Bosche M, Adelsberger JW, Sereti I, Davey RT Jr, Tavel JA, Huang CY, Issaq HJ, Fox SD, Lane HC, Kovacs JA. CD4 T cell survival after intermittent interleukin-2 therapy is predictive of an increase in the CD4 T cell count of HIV-infected patients. J Infect Dis. 2008 Sep 15;198(6):843-50.
[PubMed]


3.
Huang DW, Sherman BT, Lempicki RA. DAVID gene ID conversion tool. Bioinformation. 2008. July; 2(10): 428-430
[PubMed]


4.
Suzman DL, McLaughlin M, Hu Z, Kleiner DE, Wood B, Lempicki RA, Mican JM, Suffredini A, Masur H, Polis MA, Kottilil S. Identification of novel markers for liver fibrosis in HIV/hepatitis C virus coinfected individuals using genomics-based approach. AIDS. 2008 Jul 31;22(12):1433-9.
[PubMed]


5.
Arthos J, Cicala C, Martinelli E, Macleod K, Van Ryk D, Wei D, Xiao Z, Veenstra TD, Conrad TP, Lempicki RA, McLaughlin S, Pascuccio M, Gopaul R, McNally J, Cruz CC, Censoplano N, Chung E, Reitano KN, Kottilil S, Goode DJ, Fauci AS. HIV-1 envelope protein binds to and signals through integrin alpha4beta7, the gut mucosal homing receptor for peripheral T cells. Nature Immunol. 2008 Mar;9(3):301-9.
[PubMed]
 

6.
Tilton JC, Manion MM, Luskin MR, Johnson AJ, Patamawenu AA, Hallahan CW, Cogliano-Shutta NA, Mican JM, Davey RT Jr, Kottilil S, Lifson JD, Metcalf JA, Lempicki RA, Connors M. Human immunodeficiency virus viremia induces plasmacytoid dendritic cell activation in vivo and diminished alpha interferon production in vitro. J Virol. 2008 Apr;82(8):3997-4006.
[PubMed]


7.
Imamichi T, Yang J, Huang DW, Brann TW, Fullmer BA, Adelsberger JW, Lempicki RA, Baseler MW, Lane HC. IL-27, a novel anti-HIV cytokine, activates multiple interferon-inducible genes in macrophages. AIDS. 2008 Jan 2;22(1):39-45.
[PubMed]

2007

1.
Sherman BT, Huang DW, Tan Q,  Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA. DAVID Knowledgebase: A Gene-centered Database Integrating Heterogeneous Gene Annotation Resources to Facilitate High-throughput Gene Functional Analysis. BMC Bioinformatics. 2007 Nov 2;8(1):426.
[PubMed]


2.
Nussenblatt V, McLaughlin M, Rehm CA, Lempicki RA, Brann T, Yang J, Proschan M, Highbarger HC, Dewar RL, Imamichi T, Koratich C, Neumann AU, Masur H, Polis MA, Kottilil S. Immunodeficiency and intrinsic IFN resistance are associated with viral breakthrough to HCV therapy in HIV-coinfected patients. AIDS Res Hum Retroviruses. 2007 Nov;23(11):1354-9.
[PubMed]


3.
Kottilil S, Jackson JO, Reitano KN, O'shea MA, Roby G, Lloyd M, Yang J, Hallahan CW, Rehm CA, Arthos J, Lempicki R, Fauci AS.Innate Immunity in HIV Infection: Enhanced Susceptibility to CD95-Mediated Natural Killer Cell Death and Turnover Induced by HIV Viremia. J Acquir Immune Defic Syndr. 2007 Oct 1;46(2):151-9.
[PubMed]


4.
Ishaq M, Degray G, Mou K, Aguilera A, Yang J, Lempicki RA, Hazen A, Natarajan V.   Zap70 signaling pathway mediates glucocorticoid receptor-dependent transcriptional activation: role in the regulation of annexin 1 expression in T cells. J Immunol. 2007 Sep 15;179(6):3851-8.
[PubMed]


5.
Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA. DAVID Gene Functional Classification Tool: A novel biological module-centric algorithm to functionally analyze large gene list. Genome Biol. 2007 Sep 4;8(9):R183.
[PubMed]


6.
Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, Lempicki RA. DAVID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007 Jul 1;35.
[PubMed]


7.
Fakruddin JM, Lempicki RA, Gorelick RJ, Yang J, Adelsberger JW, Garcia-Pineres AJ, Pinto LA, Lane HC, Imamichi T.
 Noninfectious papilloma virus-like particles inhibit HIV-1 replication: implications for immune control of HIV-1 infection by IL-27. Blood. 2007 Mar 1;109(5):1841-9.
[PubMed]

2006

1.
Tilton JC, Johnson AJ, Luskin MR, Manion MM, Yang J, Adelsberger JW, Lempicki RA, Hallahan CW, McLaughlin M, Mican JM, Metcalf JA, Iyasere C, Connors M. Diminished production of monocyte proinflammatory cytokines during human immunodeficiency virus viremia is mediated by type I interferons. J Virol. 2006 Dec;80(23):11486-97.
[PubMed]


2.
Wu L, Kottilil S, Lempicki R, Yang J, McLaughlin M, Hu Z, Koratich C, Reitano KN, Rehm CA, Masur H, Wood B, Kleiner DE, Polis MA. Hepatic histologic response (HR) to combination therapy among HCV/HIV-coinfected individuals: interferon induces HR independent of sustained virologic response (SVR). AIDS Res Hum Retroviruses. 2006 Nov;22(11):1091-8.
[PubMed]


3.
Bacolla A, Collins JR, Gold B, Chuzhanova N, Yi M, Stephens RM, Stefanov S, Olsh A, Jakupciak JP, Dean M, Lempicki RA, Cooper DN, Wells RD. Long homopurine*homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region. Nucleic Acids Res. 2006 May 19;34(9):2663-75.
[PubMed]


4.
Cortez KJ, Lyman CA, Kottilil S, Kim HS, Roilides E, Yang J, Fullmer B, Lempicki R, Walsh TJ.  Functional genomics of innate host defense molecules in normal human monocytes in response to Aspergillus fumigatus. Infect Immun. 2006 Apr;74(4):2353-65. 
[PubMed]


5.
Lempicki RA, Polis MA, Yang J, McLaughlin M, Koratich C, Huang DW, Fullmer B, Wu L, Rehm CA, Masur H, Lane HC, Sherman KE, Fauci AS, Kottilil S. Gene Expression Profiles in Hepatitis C Virus (HCV) and HIV Coinfection: Class Prediction Analyses before Treatment Predict the Outcome of Anti-HCV Therapy among HIV-Coinfected Persons. J Infect Dis. 2006 Apr 15;193(8):1172-7.
[PubMed]


6.
Cicala C, Arthos J, Martinelli E, Censoplano N, Cruz CC, Chung E, Selig SM, Van Ryk D, Yang J, Jagannatha S, Chun TW, Ren P, Lempicki RA, Fauci AS. R5 and X4 HIV envelopes induce distinct gene expression profiles in primary peripheral blood mononuclear cells. Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3746-51.
[PubMed]


7.
Di Mascio M, Sereti I, Matthews LT, Natarajan V, Adelsberger J, Lempicki R, Yoder C, Jones E, Chow C, Metcalf JA, Sidorov IA, Dimitrov DS, Polis MA, Kovacs JA. Naive T-cell dynamics in human immunodeficiency virus type 1 infection: effects of highly active antiretroviral therapy provide insights into the mechanisms of naive T-cell depletion. J Virol. 2006 Mar;80(6):2665-74. 
[PubMed]


8.
Patton GW, Stephens R, Sidorov IA, Xiao X, Lempicki RA, Dimitrov DS, Shoemaker RH, Tudor G. Transcriptomic response to differentiation induction.  BMC Bioinformatics. 2006 Feb 17;7:81.
[PubMed]


9.
Cicala C, Arthos J, Censoplano N, Cruz C, Chung E, Martinelli E, Lempicki RA, Natarajan V, VanRyk D, Daucher M, Fauci AS. HIV-1 gp120 induces NFAT nuclear translocation in resting CD4+ T-cells. Virology. 2006 Feb 5;345(1):105-14.
[PubMed]


10.
 Kottilil S, Shin K, Jackson JO, Reitano KN, O'Shea MA, Yang J, Hallahan CW, Lempicki R, Arthos J, Fauci AS. Innate immune dysfunction in HIV infection: effect of HIV envelope-NK cell interactions. J Immunol. 2006 Jan 15;176(2): 1107-14.
[PubMed]

2005

1.
Xiao X, Sidorov IA, Gee J, Lempicki RA, Dimitrov DS.  Retinoic acid-induced downmodulation of telomerase activity in human cancer cells. Exp Mol Pathol. 2005 Oct;79(2):108-17. 
[PubMed]


2.
Kovacs JA, Lempicki RA, Sidorov IA, Adelsberger JW, Sereti I, Sachau W, Kelly G, Metcalf JA, Davey RT Jr, Falloon J, Polis MA, Tavel J, Stevens R, Lambert L, Hosack DA, Bosche M, Issaq HJ, Fox SD, Leitman S, Baseler MW, Masur H, Di Mascio M, Dimitrov DS, Lane HC.  Induction of prolonged survival of CD4+ T lymphocytes by intermittent IL-2 therapy in HIV-infected patients. J Clin Invest. 2005 Aug;115(8):2139-48
[PubMed]

2004

1.
Sereti I, Anthony KB, Martinez-Wilson H, Lempicki R, Adelsberger J, Metcalf JA, Hallahan CW, Follmann D, Davey RT, Kovacs JA, Lane HC. IL-2-induced CD4+ T-cell expansion in HIV-infected patients is associated with long-term decreases in T-cell proliferation. Blood. 2004 Aug 1;104(3):775-80. Epub 2004 Apr 13. 
[PubMed]

2003

1.
Becker KG, Hosack DA, Dennis G Jr, Lempicki RA, Bright TJ, Cheadle C, Engel J.  PubMatrix: a tool for multiplex literature mining. BMC Bioinformatics. 2003 Dec 10;4:61. 
[PubMed]


2.
Hawse JR, Hejtmancik JF, Huang Q, Sheets NL, Hosack DA, Lempicki RA, Horwitz J, Kantorow M.  Identification and functional clustering of global gene expression differences between human age-related cataract and clear lenses. Mol Vis. 2003 Oct 7;9:515-37.
[PubMed]


3.
Tan PK, Downey TJ, Spitznagel EL Jr, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 2003 Oct 1;31(19):5676-84.  [PubMed]


4.
Chun TW, Justement JS, Lempicki RA, Yang J, Dennis G Jr, Hallahan CW, Sanford C, Pandya P, Liu S, McLaughlin M, Ehler LA, Moir S, Fauci AS.  Gene expression and viral prodution in latently infected, resting CD4+ T cells in viremic versus aviremic HIV-infected individuals. Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1908-13. Epub 2003 Jan 27.
 [PubMed]


5.
Hosack DA, Dennis G Jr, Sherman BT, Lane HC, Lempicki RA. Identifying biological themes within lists of genes with EASE. Genome Biol. 2003;4(10):R70. Epub 2003 Sep 11. 
[PubMed]


6.
Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA.  DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003;4(5):P3. Epub 2003 Apr 3.
[PubMed]


7.
Hengel RL, Thaker V, Pavlick MV, Metcalf JA, Dennis G Jr, Yang J, Lempicki RA, Sereti I, Lane HC. Cutting edge: L-selectin (CD62L) expression distinguishes small resting memory CD4+ T cells that preferentially respond to recall antigen. J Immunol. 2003 Jan 1;170(1):28-32. 
[PubMed]


8.
Imamichi T, Murphy MA, Adelsberger JW, Yang J, Watkins CM, Berg SC, Baseler MW, Lempicki RA, Guo J, Levin JG, Lane HC. Actinomycin D induces high-level resistance to thymidine analogs in replication of human immunodeficiency virus type 1 by interfering with host cell thymidine kinase expression. J Virol. 2003 Jan;77(2):1011-20. 
[PubMed]

2002

1.
Xiao X, Phogat SK, Sidorov IA, Yang J, Horikawa I, Prieto D, Adelesberger J, Lempicki R, Barrett JC, Dimitrov DS. Identification and characterization of rapidly dividing U937 clones with differential telomerase activity and gene expression profiles: role of c-Myc/Mad1 and Id/Ets proteins. Leukemia. 2002 Sep;16(9):1877-80.
[PubMed]


2.
Natarajan V, Lempicki RA, Sereti I, Badralmaa Y, Adelsberger JW, Metcalf JA, Prieto DA, Stevens R, Baseler MW, Kovacs JA, Lane HC. Increased peripheral expansion of naive CD4+ T cells in vivo after IL-2 treatment of patients with HIV infection. Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10712-7.
[PubMed]


3.
Ishibe N, Prieto D, Hosack DA, Lempicki RA, Goldin LR, Raffeld M, Marti GE, Caporaso NE. Telomere length and heavy-chain mutation status in familial chronic lymphocytic leukemia. Leuk Res. 2002 Sep;26(9):791-4.
[PubMed]
 

4.
Cicala C, Arthos J, Selig SM, Dennis G Jr, Hosack DA, Van Ryk D, Spangler ML, Steenbeke TD, Khazanie P, Gupta N, Yang J, Daucher M, Lempicki RA, Fauci AS. HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication. Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9380-5.
[PubMed]
 

5.
Sidorov, I.A., Hosack, D.A., Gee, D., Yang, J., Cam, M.C., Lempicki, R.A., Dimitrov, D.S. Oligonucleotide microarray data distribution and normalization, Information Sciences 2002 146(1-4): 67-73.
[Link]
 
2001

1.
Kovacs JA, Lempicki RA, Sidorov IA, Adelsberger JW, Herpin B, Metcalf JA, Sereti I, Polis MA, Davey RT, Tavel J, Falloon J, Stevens R, Lambert L, Dewar R, Schwartzentruber DJ, Anver MR, Baseler MW, Masur H, Dimitrov DS, Lane HC. Identification of dynamically distinct subpopulations of T lymphocytes that are differentially affected by HIV. J Exp Med. 2001 Dec 17;194(12):1731-41.
[PubMed]


2.
Douek DC, Betts MR, Hill BJ, Little SJ, Lempicki R, Metcalf JA, Casazza J, Yoder C, Adelsberger JW, Stevens RA, Baseler MW, Keiser P, Richman DD, Davey RT, Koup RA. Evidence for increased T cell turnover and decreased thymic output in HIV infection. J Immunol. 2001 Dec 1;167(11):6663-8.
[PubMed]


3.
Kovacs JA, Vogel S, Metcalf JA, Baseler M, Stevens R, Adelsberger J, Lempicki R, Hengel RL, Sereti I, Lambert L, Dewar RL, Davey RT Jr, Walker RE, Falloon J, Polis MA, Masur H, Lane HC. Interleukin-2 induced immune effects in human immunodeficiency virus-infected patients receiving intermittent interleukin-2 immunotherapy. Eur J Immunol. 2001 May;31(5):1351-60.
[PubMed]


4.
(Book Chapter) D.S. Dimitrov, I.A. Sidorov, Y. Endo, T. Igarashi, R.A. Lempicki, J. Kovacs, R.T. Davey, J. Lifson, M.A. Martin and H.C. Lane. DYNAMICS MODELS OF VIRUS/CELL TURNOVER IN HIV INFECTIONS.  Proc. Atl. Symp. Comput. Biol. Genome Information Systems and Technology (CBGIST 2001), Eds. Wu, C.H., Wang, P.P, Wang, J.T.L., Durham, pp. 200-204, 2001.

2000

1.
Lempicki RA, Kovacs JA, Baseler MW, Adelsberger JW, Dewar RL, Natarajan V, Bosche MC, Metcalf JA, Stevens RA, Lambert LA, Alvord WG, Polis MA, Davey RT, Dimitrov DS, Lane HC. Impact of HIV-1 infection and highly active antiretroviral therapy on the kinetics of CD4+ and CD8+ T cell turnover in HIV-infected patients. Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13778-83.
[PubMed]
 

2.
Carpenter S, Vaughn EM, Yang J, Baccam P, Roth JA, Wannemuehler Y., Antigenic and genetic stability of bovine immunodeficiency virus during long-term persistence in cattle experimentally infected with the BIV(R29) isolate. J Gen Virol 2000 Jun;81:1463-1472.
[PubMed]
 
1999

1.
Davey RT, Jr,Bhat N, Yoder C, Chun TW, Metcalf JA, Dewar R, Natarajan V, Lempicki RA, Adelsberger JW, Miller KD, Kovacs JA, Polis MA, Walker RE, Falloon J, Masur H, Gee D, Baseler M, Dimitrov DS, Fauci AS, Lane HC. HIV-1 and T cell dynamics after interruption of highly active antiretroviral therapy (HAART) in patients with a history of sustained viral suppression.  Proc Natl Acad Sci 1999 96(26):15109-14.
[PubMed]








 Please cite Nature Protocols 2009; 4(1):44 & Nucleic Acids Res. 2009;37(1):1 within any publication that makes use of any methods inspired by DAVID.
                          

        

                 
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